Question: Polymorphism and SNPs
0
gravatar for onemoreuser
2.7 years ago by
onemoreuser10
onemoreuser10 wrote:

This is a theory question. I want to know the difference between a Single Nucleotide Polymorphism and a Polymorphism. They are not exactly the same thing but I can't understand the difference. SNP is a single nucleotide change that occurs in a population with a frequency >=1% (by the conventional definition). Now, a polymorphism isn't also a change that can occur in a population?

snp genetics polymorphism • 785 views
ADD COMMENTlink modified 2.7 years ago by Denise - Open Targets4.8k • written 2.7 years ago by onemoreuser10
0
gravatar for igor
2.7 years ago by
igor7.4k
United States
igor7.4k wrote:

It depends on the particular field. Different groups use slightly different definitions of SNPs.

For example, I've seen SNP where S stands "small", not "single", which would include indels. Also, a SNP may be considered a SNP regardless of its population frequency as long as it's germline.

ADD COMMENTlink written 2.7 years ago by igor7.4k
0
gravatar for Denise - Open Targets
2.7 years ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets4.8k wrote:

I'd think that every SNP is a polymorphism, but not all polymorphisms are SNPs, as they can be indels or CNV (copy number variants/variation), for example. The word 'polymorphism' comes from the Greek: poly: several; morphe: forms, states. I'm not sure if the word polymorphism is standard in the Sequence Ontology (SO) project. You can search for it, but you will get redirected to SNV (single nucleotide variants) for example rather than SNP. The latter is rather well established in the literature and scientific usage but SO and others may try to avoid using that term. For example, Ensembl avoids using the word polymophism and use the word variant instead. I think in the past polymophism was used to differentiate from mutation, the latter would cause a disease but not the former.

ADD COMMENTlink written 2.7 years ago by Denise - Open Targets4.8k

On the other hand, NCBI's dbSNP (even have a SNP in the name) contains both disease-causing and non-disease-causing SNPs and they refer to both as SNPs.

ADD REPLYlink written 2.7 years ago by igor7.4k

Yes, I know. This shows how no consensus is out there. I thought that dbSNP used to have just SNPs but now it's got indels. Therefore it's called Short Genetic Variations. I'd have guessed that a variant could be identified by someone and submitted to dbSNP. Later down the line, it could turn out that this variant is associated with cancer (somatic mutation?). So in addition to its original rsID, it will have another ID, for example CM (coming from mutation databases such as COSMIC and HGMD).

ADD REPLYlink written 2.7 years ago by Denise - Open Targets4.8k
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